endixk
`calculate` error when using `-p blastp`
Thanks for your help with the previous issue - I'm back with a different one!
I'd like to use blastp for some AAI calculations. I used conda to install blastp in the same environment I was previously using for EzAAI calculations (info below). I'm running a single instance at a time.
As I understand it, I use the same extract command to prepare databases, regardless of mapping type - is that incorrect?
Using the sample data from your tutorial:
java -jar EzAAI_v1.11.jar calculate -i db/Ci.db -j db/Lc.db \
-t 10 -p blastp -o test.blastp.tsv -v
I get the following error:
[FEB 24 08:51:15] EzAAI |: EzAAI - v1.11 [Feb. 2022]
getEngineName() called
[FEB 24 08:51:16] EzAAI |: Calculating AAI... [Task 1/1]
[FEB 24 08:51:16] EzAAI |: Preparing to run reciprocal BLASTp+...
[FEB 24 08:51:16] EzAAI |: Running BLASTp+... (/tmp/bdd397448b571442_faa/i0.faa vs. /tmp/bdd397448b571442_faa/j0.faa)
java.io.FileNotFoundException: /tmp/bdd397448b571442_vice.out (No such file or directory)
at java.base/java.io.FileInputStream.open0(Native Method)
at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
at java.base/java.io.FileReader.<init>(FileReader.java:75)
at leb.process.ProcFuncAnnoByBlastPlus.parseOutFile(ProcFuncAnnoByBlastPlus.java:283)
at leb.process.ProcFuncAnnoByBlastPlus.execute(ProcFuncAnnoByBlastPlus.java:273)
at leb.process.ProcCalcPairwiseAAI.pairwiseBlastp(ProcCalcPairwiseAAI.java:499)
at leb.process.ProcCalcPairwiseAAI.calculateProteomePairWithDetails(ProcCalcPairwiseAAI.java:248)
at leb.main.EzAAI.runCalculate(EzAAI.java:361)
at leb.main.EzAAI.run(EzAAI.java:493)
at leb.main.EzAAI.main(EzAAI.java:528)
[FEB 24 08:51:16] ERROR |: Program terminated with error.
Please let me know if you have ideas on how to proceed. Thanks!
Conda environment:
conda list -p /home/ntpierce/miniconda3/066c58eb7ac25d2ab6a302135cb3ad40
# packages in environment at /home/ntpierce/miniconda3/066c58eb7ac25d2ab6a302135cb3ad40:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
blast 2.12.0 h3289130_3 bioconda
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
curl 7.81.0 h494985f_0 conda-forge
entrez-direct 16.2 he881be0_0 bioconda
gawk 5.1.0 h7f98852_0 conda-forge
gettext 0.19.8.1 h73d1719_1008 conda-forge
krb5 1.19.2 h48eae69_3 conda-forge
libcurl 7.81.0 h494985f_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_12 conda-forge
libgomp 11.2.0 h1d223b6_12 conda-forge
libidn2 2.3.2 h7f98852_0 conda-forge
libnghttp2 1.46.0 ha19adfc_0 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_12 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
mmseqs2 13.45111 h95f258a_1 bioconda
ncurses 6.3 h9c3ff4c_0 conda-forge
openssl 3.0.0 h7f98852_2 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
perl 5.32.1 1_h7f98852_perl5 conda-forge
perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda
perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge
perl-common-sense 3.75 pl5321hdfd78af_0 bioconda
perl-compress-raw-bzip2 2.101 pl5321h1b792b2_0 bioconda
perl-compress-raw-zlib 2.101 pl5321h1b792b2_1 bioconda
perl-encode 3.16 pl5321h779adbc_0 bioconda
perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge
perl-exporter-tiny 1.002002 pl5321hdfd78af_0 bioconda
perl-extutils-makemaker 7.64 pl5321hd8ed1ab_0 conda-forge
perl-io-compress 2.102 pl5321h1b792b2_0 bioconda
perl-io-zlib 1.11 pl5321hdfd78af_0 bioconda
perl-json 4.05 pl5321hdfd78af_0 bioconda
perl-json-xs 2.34 pl5321h7d875b9_4 bioconda
perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda
perl-list-moreutils-xs 0.430 pl5321h779adbc_0 bioconda
perl-parent 0.238 pl5321hd8ed1ab_0 conda-forge
perl-pathtools 3.75 pl5321h779adbc_2 bioconda
perl-scalar-list-utils 1.60 pl5321h779adbc_0 bioconda
perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda
prodigal 2.6.3 h779adbc_3 bioconda
tk 8.6.11 h27826a3_1 conda-forge
wget 1.20.3 ha35d2d1_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
Hello again,
I've checked your issue and indeed the program did not properly worked with BLASTp+.
The issue was occurred since the program was trying to handle multiple binary paths with single variable, therefore being confused identifying the proper path it should use.
In your case, the program tried to run mmseqs binary to which the proper command should use blastp binary.
I have modified the program a little bit to adjust this problem, by providing independent path for each dependent program.
Again, you can download the newer version (v1.12) using this link.
Thank you so much for hunting down the issues that I have overlooked.
Regards, Daniel
